1APB

A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Pro to Gly mutation in the hinge of the arabinose-binding protein enhances binding and alters specificity. Sugar-binding and crystallographic studies.

Vermersch, P.S.Tesmer, J.J.Lemon, D.D.Quiocho, F.A.

(1990) J.Biol.Chem. 265: 16592-16603

  • Primary Citation of Related Structures:  1BAP, 9ABP

  • PubMed Abstract: 
  • The L-arabinose-binding protein (ABP) of Escherichia coli consists structurally of two distinct globular domains connected by a hinge of three separate peptide segments. Arabinose is bound and completely sequestered within the deep cleft between the ...

    The L-arabinose-binding protein (ABP) of Escherichia coli consists structurally of two distinct globular domains connected by a hinge of three separate peptide segments. Arabinose is bound and completely sequestered within the deep cleft between the two domains. With reduced affinity, ABP also binds D-galactose (approximately 2-fold reduction) and D-fucose (approximately 40-fold reduction). Experiments have been conducted to explore the role in sugar binding of the hinge connecting the two domains of ABP. To increase the flexibility of the hinge region, a glycine was substituted for a proline at position 254 by site-directed mutagenesis. Unexpectedly, this mutation resulted in the dramatic enhancement of galactose binding over that of arabinose. The affinity of the mutant ABP for galactose increased by over 20-fold, while that for arabinose and fucose remained relatively unchanged. We have measured association and dissociation rates of the Gly-254 ABP with L-arabinose, D-galactose, and D-fucose and have determined the crystallographic structure of the protein complexed with each of the three sugars. Both the ligand-binding kinetic measurements and structure analysis indicate that the altered specificity is due to an effective increase in the rigidity of the hinge in the closed conformation which is induced upon galactose binding. Stabilizing contacts are formed between the strands of the hinge in the Gly-254 ABP when galactose is bound which are not found in complexes with the other sugars or the liganded wild-type protein.


    Related Citations: 
    • Structure of L-Arabinose-Binding Protein from Escherichia Coli at 5 Angstroms Resolution and Preliminary Results at 3.5 Angstroms
      Phillips Jr., G.N.,Mahajan, V.K.,Siu, A.K.Q.,Quiocho, F.A.
      (1976) Proc.Natl.Acad.Sci.USA 73: 2186
    • Location of the Sugar-Binding Site of L-Arabinose-Binding Protein. Sugar Derivative Syntheses, Sugar Binding Specificity, and Difference Fourier Analyses
      Newcomer, M.E.,Miller /III, D.M.,Quiocho, F.A.
      (1979) J.Biol.Chem. 254: 7529
    • Structure of the L-Arabinose-Binding Protein from Escherichia Coli at 2.4 Angstroms Resolution
      Gilliland, G.L.,Quiocho, F.A.
      (1981) J.Mol.Biol. 146: 341
    • L-Arabinose-Binding Protein-Sugar Complex at 2.4 Angstroms Resolution. Stereochemistry and Evidence for a Structural Change
      Newcomer, M.E.,Gilliand, G.L.,Quiocho, F.A.
      (1981) J.Biol.Chem. 256: 13213
    • The 2.8-Angstroms Resolution Structure of the L-Arabinose-Binding Protein from Escherichia Coli
      Quiocho, F.A.,Gilliland, G.L.,Phillips Jr., G.N.
      (1977) J.Biol.Chem. 252: 5142
    • Novel Stereospecificity of the L-Arabinose-Binding Protein
      Quiocho, F.A.,Vyas, N.K.
      (1984) Nature 310: 381
    • Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules
      Quiocho, F.A.,Wilson, D.K.,Vyas, N.K.
      (1989) Nature 340: 404
    • The Thiol Group of the L-Arabinose-Binding Protein. Chromophoric Labeling and Chemical Identification of the Sugar-Binding Site
      Miller /III, D.M.,Newcomer, M.E.,Quiocho, F.A.
      (1979) J.Biol.Chem. 254: 7521
    • The Radius of Gyration of L-Arabinose-Binding Protein Decreases Upon Binding of Ligand
      Newcomer, M.E.,Lewis, B.A.,Quiocho, F.A.
      (1981) J.Biol.Chem. 256: 13218
    • Hinge-Bending in L-Arabinose-Binding Protein. The "Venus'S-Flytrap" Model
      Mao, B.,Pear, M.R.,Mccammon, J.A.,Quiocho, F.A.
      (1982) J.Biol.Chem. 257: 1131


    Organizational Affiliation

    Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-ARABINOSE-BINDING PROTEIN
A
306Escherichia coli (strain K12)Gene Names: araF
Find proteins for P02924 (Escherichia coli (strain K12))
Go to UniProtKB:  P02924
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FCB
Query on FCB

Download SDF File 
Download CCD File 
A
BETA-D-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-FPRJBGLDSA-N
 Ligand Interaction
FCA
Query on FCA

Download SDF File 
Download CCD File 
A
ALPHA-D-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-PHYPRBDBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FCAKd: 1510 nM BINDINGMOAD
FCBKd: 1510 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.460α = 90.00
b = 71.820β = 90.00
c = 77.840γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-01-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance